Insurgent activities included the burning of Thai flags and the raising of Malaysian national flags in many areas of four provinces - Narathiwat, Yala, Pattani and Songkhla.
The unrest came on the 50th anniversary of Malaysia's independence from British rule and the anniversary of the founding of the Bersatu separatist movement.
Suspicious objects were found in many locations; some were fake bombs but most were real explosives.
In Narathiwat, bomb squads took about three hours to defuse them. Six soldiers were wounded in bomb blasts in separate locations in the province.
Malaysian flags were displayed at various locations, along roads, on trees and electricity poles. Tyres were burned and spikes were strewn on roads.
Police also seized dozens of cloth banners with messages ridiculing and challenging authorities. One read: "Welcome, EOD [explosive ordnance disposal]". Another read: "Without GT200 [the controversial bomb detector], what will you rely on?"
The Internal Security Operations Command Region 4 yesterday played down the incidents.
Isoc Region 4 deputy spokesman Promote Prom-in said a probe indicated a plot had been hatched to cause disturbances and attract media attention.
The torching of Thai flags and hoisting of Malaysian ones were believed to be an effort to undermine the relationship between Thailand and Malaysia, he said.
"But these kind of incidents can't make us turn against each other," Col Promote said. "We have maintained a good relationship at the operational and policy levels."
He said the activities might be intended to discredit Thailand as it prepared to become part of the Asean Economic Community, starting in 2015. But Panitan Wattanayagorn, Chulalongkorn University's political scientist who has expertise in security issues, said the spate of disruptive acts reflected authorities' failure to implement strategies to deal with violence in the South.
"Our security measures in the deep South are lagging behind the insurgents' operations," Mr Panitan said, adding that the army and the government should work closely to come up with new and effective measures.
Mr Panitan proposed that border patrol police officers should be deployed to work with local police as these police officers have been trained specifically for the restive areas and local communities.
Mr Panitan said he agreed with the government's attempt to set up a new command centre in Bangkok to coordinate the work at the Isoc.
"But what I am worried is that the new centre will just cause more red tape," he said.
He added that the Thai government should ask Malaysia to help crack down on all suspected Thai-Muslim people who fled into hiding in Malaysia.
"These are very well-coordinated attacks and it is not easy in a short time to carry out such attacks," Mr Panitan said. "This situation tells us that there are many members of separatist groups in the far South who are actively calling for freedom and autonomy.
"The burning of Thai flags and putting up of Malaysian flags are symbolic acts to show the government that the separatist movement remains intact in the area. They are waiting for the day that they can put up their own flags."
Boonsom Thongsriprai, chairman of the Federation of the Three Southern Border Provinces Teachers, said the activities were intended to demonstrate the strength of the insurgency.
Isara News Agency, focusing on southern violence coverage yesterday, gathered observations from the South about the wave of insurgent incidents, casting doubt on the government's handling of the southern problem.
It pointed out that hoisting flags took time and resources but the militants seemed to have managed to operate without any disruption.
An operation of this scale required the use of vehicles, particularly pickup trucks, to transport men and equipment. These vehicles seemed to simply cruise past the security checkpoints that were said to be located in 66 spots across the region.
The incidents in Yala municipal area suggested a security lapse and called into question a claim that security patrols take place around the clock.
A warning had been issued on Thursday night that attacks might take place to mark the anniversary of the founding of the Bersatu movement yesterday.
The fact that the incidents took place in so many areas indicated the insurgent movement's wide base of support.
The activities also cast doubts on the state's claim about the number of insurgents and sympathisers, which was estimated at 9,000.
Prime Minister Yingluck Shinawatra has ordered the secretary-general of the National Security Council, Wichean Potephosree, to go to the South to help oversee the situation there.
Deputy Prime Minister Yutthasak Sasiprapa, who is in charge of security affairs, said officials in the deep South were checking footage from closed circuit television cameras.
"I don't think these incidents will hurt Thai-Malaysian ties and we're telling Malaysia that the Bersatu is trying to get the Malaysian people involved [in the southern insurgency]," Gen Yutthasak said.